Structural and Functional Analysis of the Amorphous Calcium Carbonate-Binding Protein Paramyosin in the Shell of the Pearl Oyster, Pinctada fucata.

Amorphous calcium carbonate (ACC) is an important precursor phase for the formation of aragonite crystals in the shells of Pinctada fucata. To identify the ACC-binding protein in the inner aragonite layer of the shell, extracts from the shell were used in the ACC-binding experiments. Semiquantitative analyses using liquid chromatography-mass spectrometry revealed that paramyosin was strongly associated with ACC in the shell. We discovered that paramyosin, a major component of the adductor muscle, was included in the myostracum, which is the microstructure of the shell attached to the adductor muscle. Purified paramyosin accumulates calcium carbonate and induces the prism structure of aragonite crystals, which is related to the morphology of prism aragonite crystals in the myostracum. Nuclear magnetic resonance measurements revealed that the Glu-rich region was bound to ACC. Activity of the Glu-rich region was stronger than that of the Asp-rich region. These results suggest that paramyosin in the adductor muscle is involved in the formation of aragonite prisms in the myostracum.

Optimization of reverse NOE pumping experiments in the analysis of complex systems with densely crowded NMR spectra.

We present an optimization of Reverse NOE-pumping (RNP) in order to observe the 1H signals of ligands bound to proteins. Although various ligand-based NMR screening methods have been proposed, the most frequently used method has been Saturation-Transfer Difference (STD), owing to the relatively easy setup of experiments. Yet the critical point of STD is the selective irradiation of protein without irradiating ligand, and thus the STD technique is unable to observe 1H ligand signals, which resonate across the entire 1H spectral width. In the present study, the RNP experiment has been improved to develop an effective NMR-based screening technique. The optimized RNP spectra reveal less subtraction artifacts and phase distortion than the original RNP spectra, indicating its applicability to any type of ligand molecules.

NMR screening method based on 19F spin-spin relaxation time for analyses of fluorinated compound bound to proteins.

NMR screening methods based on 19F spin-spin relaxation time (19F-T2) were applied to fluorinated compounds bound to human serum albumin. Diflunisal and fleroxacin (the fluorinated compounds) contain two and three fluorine atoms per molecule, respectively, and are suitable as the model system for 19F NMR analysis. It was shown that 19F-T2 was more sensitive in monitoring the binding affinity to the target protein than 19F spin-lattice relaxation time (19F-T1). The comparisons of 19F signal intensities acquired at different echo times using 19F-T2 pulse sequence were also shown to be an effective means of assessing complex formation for fluorinated compounds.

NMR and HPLC profiling of bee pollen products from different countries.

Bee pollen, a beehive product collected from flowers by honeybees, contains over 250 biological substances, and has attracted increasing attention as a functional food. However, commercial bee pollen products are often multifloral, and samples from different countries vary significantly. There is no universal standard for objective quality assessment of bee pollen based on its chemical composition. Here, we report metabolomic analysis of 11 bee pollen samples from Spain, China, and Australia for quality control. The characteristics of the samples depend on the sucrose, nucleoside, amino acid, and flavanol concentrations. Bee pollen samples from Spain and Australia had higher sucrose and adenosine concentrations, whereas those from China had higher trigonelline, uridine, and cytidine concentrations. Interestingly, acetic acid was only detected in samples from China. These components can be used to identify the country of origin. The obtained profiles of the samples will contribute to universal standard development for bee pollen products.

Development of 1H{19F} saturation transfer difference experiments for detection of a fluorinated compound bound to proteins.

The 1H{19F} saturation transfer difference (STD) experiment presented here incorporates the WATERGATE W5 sequence to observe protein-ligand interactions in a human serum albumin (HSA)-fleroxacin complex. In conventional STD experiments, 1H of proteins are first saturated, and the ligands bound to these proteins are then observed. The method proposed here reverses this process: fluorine atoms in fleroxacin are selectively saturated, and saturation transfer then occurs to protons of fleroxacin as well as to those of HSA. The combined use of the present 1H{19F} STD and conventional STD methods is expected to provide better insight in the analysis of the role of fluorine atoms in a fluorinated compound.

Myrindole A, an Antimicrobial Bis-indole from a Marine Sponge Myrmekioderma sp.

Myrindole A, a bis-indole alkaloid, was isolated from the deep-sea sponge Myrmekioderma sp. The high degree of unsaturation of the molecule complicated the assignment of its structure by standard 2D-NMR experiments but was ultimately achieved by a combination of 1H-15N-HMBC and 1,n-ADEQUATE experiments as well as the comparison of measured and calculated CD spectra. Myrindole A showed antimicrobial activity against Gram-positive and Gram-negative bacteria.

Analysis of Binding Mode of 2'-GMP to Proteins Using 1H/31P NMR Spectroscopy.

1H/31P NMR techniques were applied to analyze the binding mode of guanosine 2'-monophosphate (2'-GMP) to histone. To date, no structures of the complex comprising 2'-GMP and histone have been deposited in Protein Data Bank. Because the 31P nucleus can be a selective marker of phosphorylated compounds, the combined use of 1H and 31P NMR spectroscopy has been applied to investigate these molecular interactions. The complex formation was initially confirmed by 31P-diffusion ordered spectroscopy and 31P-T1 measurements. In 1H{1H} saturation transfer difference experiments, H2' and H3' signals of 2'-GMP were significantly attenuated, while the rest of the unexchangeable protons were observed, indicating that the contribution of H2' and H3' to the binding epitopes was low. The WaterLOGSY-type experiment with 31P detection also indicated that a phosphorylated group located close to H2' and H3' had little access to histone.

Author Correction: Formation of gold nanoparticles by glycolipids of Lactobacillus casei.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Identification of Binding Epitopes of a Fluorinated Compound Bound to Proteins Using 1H and 19F NMR Spectroscopy.

1H/19F NMR-based screening methods were applied to a human serum albumin-fleroxacin complex. Fleroxacin contains three fluorine atoms in a molecule, which is suitable as a model fluorinated compound for NMR analysis with 1H and 19F detection. The 19F{1H} and 1H{1H} saturation transfer difference spectra were acquired and the 1H/19F spin-lattice relaxation rates were measured with and without any selective irradiation of protein resonance to identify the binding epitopes of fleroxacin. Because several 1H signals of fleroxacin resonated close to water, its precise signal intensities were unavailable. The 19F NMR-based screening methods successfully provide complementary information, indicating its importance in the analysis of fluorinated compounds.

NMR-based metabolic profiling and comparison of Japanese persimmon cultivars.

Persimmons are a traditional, autumnal, and healthy fruit commonly consumed in Japan and East Asia based on the saying, "a persimmon a day keeps the doctor away." The differences in metabolites among five major Japanese persimmon cultivars were investigated using a nuclear magnetic resonance (NMR)-based metabolomics approach. By using a broadband water suppression enhanced through T1 effects (WET) method for the sensitive detection of minor metabolites, better discrimination among cultivars and more informative details regarding their metabolic differences have been achieved compared to those achieved in conventional 1H NMR sequences. Among the nonastringent cultivars analyzed, the Taishu cultivar has the highest abundance of amino acids. The Matsumotowase-Fuyu cultivar contains ethyl-ß-glycosides as characteristic components, which may relate to fruit softening. Citric acid concentration is higher in Maekawa Jiro than in other nonastringent cultivars. Among the two astringent cultivars analyzed, ethanol was significantly higher in Hiratanenashi than in Yotsumizo, which indicates different reactivity during deastringency treatments. The present study proposes an efficient and relatively quantitative metabolomics approach based on broadband WET NMR spectra.

DPFGSE-MDEC-J-resolved COSY: An efficient method for selectively measuring proton-proton spin coupling constants of the multiplet signals.

Natural products such as polyketides often possess various spin systems, consisting of a methine group directly bonded to a methyl group (e.g., ─CHA ─CHB (CH3 )─CHC ─). The methine proton HB splits into a broadened multiplet by coupling with several vicinal protons, rendering analysis difficult of n JH-H with respect to HB in double-quantum filtered COSY or exclusive COSY. For the purpose of measuring n JH-H in the aforesaid spin system, we have developed new techniques, named multifrequency homo-decoupling (MDEC)-J-resolved COSY and DPFGSE-MDEC-J-resolved COSY. This method incorporates MDEC pulse scheme into J-resolved COSY for the selective decouple of individual methyl groups, avoiding decoupling of the target protons resonating in methyl region. Determinations of n JH-H of the multiplet signals can easily be performed using the proposed pulse sequence.

Exploring an Artificial Metabolic Route in Fusarium sporotrichioides: Production and Characterization of 7-Hydroxy T-2 Toxin.

An artificial metabolic route to an unnatural trichothecene was designed by taking advantage of the broad substrate specificities of the T-2 toxin biosynthetic enzymes of Fusarium sporotrichioides. By feeding 7-hydroxyisotrichodermin, a shunt pathway metabolite of F. graminearum, to a trichodiene synthase-deficient mutant of F. sporotrichioides, 7-hydroxy T-2 toxin (1) was obtained as the final metabolite. Such an approach may have future applications in the metabolic engineering of a variety of fungal secondary metabolites. The toxicity of 7-hydroxy T-2 toxin was 10 times lower than that of T-2 toxin in HL-60 cells.

Solution-state structures of the cellulose model pullulan in lithium chloride/N,N-dimethylacetamide.

Pullulan is soluble in both N,N-dimethylacetamide (DMAc) and LiCl/DMAc. Here, the solution-state structures of pullulan in these two solvents were studied by size-exclusion chromatography with multi-angle laser light scattering (SEC/MALLS) and nuclear magnetic resonance (NMR) analyses. SEC/MALLS and off-line refractive index analyses revealed that the hydroxy groups of pullulan interact with LiCl in DMAc, as observed previously for cellulose. The nine different COH protons of pullulan in DMAc and LiCl/DMAc appeared independently in NMR spectra and were successfully assigned. When LiCl was present, the degree of dissociation of all COH protons of pullulan was increased by Li+ and Cl- ions, and the conformations of the COH groups became stable and restricted in DMAc. Based on the obtained results, the solution-state structures of cellulose in LiCl/DMAc are hypothesized to contain similar interactions between the cellulose hydroxy groups, and Li+ and Cl- in LiCl/DMAc to those observed for pullulan.

Formation of gold nanoparticles by glycolipids of Lactobacillus casei.

Gold nanoparticles have particular properties distinct from those of bulk gold crystals, and such nanoparticles are used in various applications in optics, catalysis, and drug delivery. Many reports on microbial synthesis of gold nanoparticles have appeared. However, the molecular details (reduction and dispersion) of such synthesis remain unclear. In the present study, we studied gold nanoparticle synthesis by Lactobacillus casei. A comparison of L. casei components before and after addition of an auric acid solution showed that the level of unsaturated lipids decreased significantly after addition. NMR and mass spectrum analysis showed that the levels of diglycosyldiacylglycerol (DGDG) and triglycosyldiacylglycerol (TGDG) bearing unsaturated fatty acids were much reduced after formation of gold nanoparticles. DGDG purified from L. casei induced the synthesis of gold nanoparticles in vitro. These results suggested that glycolipids, such as DGDG, play important roles in reducing Au(III) to Au(0) and in ensuring that the nanoparticles synthesized remain small in size. Our work will lead to the development of novel, efficient methods by which gold nanoparticles may be produced by, and accumulated within, microorganisms.

Use of NMR-Based Metabolomics To Chemically Characterize the Roasting Process of Chicory Root.

Roasted chicory root (Cichorium intybus) has been widely accepted as the most important coffee substitute. In this study, a nuclear magnetic resonance (NMR)-based comprehensive analysis was performed to monitor the substantial changes in the composition of chicory root during the roasting process. A detailed signal assignment of dried raw and roasted chicory roots was carried out using 1H, 13C, 1H-1H DQF-COSY, 1H-13C edited-HSQC, 1H-13C CT-HMBC, and 1H-13C HSQC-TOCSY NMR spectra. On the basis of the signal assignments, 36 NMR-visible components were monitored simultaneously during roasting. Inulins, sucrose, and most of the amino acids were largely degraded during the roasting process, whereas monosaccharides decreased at the beginning and then increased until the dark roasting stage. Acetamide, 5-hydroxymethylfurfural, di-d-fructose dianhydride, and norfuraneol were newly formed during roasting. Furthermore, a principal component analysis score plot indicated that similar chemical composition profiles could be achieved by roasting the chicory root either at a higher firepower for a shorter time or at a lower firepower for a longer time.

Exploring Peptide Ligase Orthologs in Actinobacteria-Discovery of Pseudopeptide Natural Products, Ketomemicins.

We recently identified a novel peptide ligase (PGM1), an ATP-grasp-ligase, that catalyzes amide bond formation between (S)-2-(3,5-dihydroxy-4-methoxyphenyl)-2-guanidinoacetic acid and ribosomally supplied oligopeptides in pheganomycin biosynthesis. This was the first example of an ATP-grasp-ligase utilizing peptides as nucleophiles. To explore the potential of this type of enzyme, we performed a BLAST search and identified many orthologs. The orthologs of Streptomyces mobaraensis, Salinispora tropica, and Micromonospora sp. were found in similar gene clusters consisting of six genes. To probe the functions of these genes, we heterologously expressed each of the clusters in Streptomyces lividans and detected novel and structurally similar pseudotripeptides in the broth of all transformants. Moreover, a recombinant PGM1 ortholog of Micromonospora sp. was demonstrated to be a novel dipeptide ligase catalyzing amide bond formation between amidino-arginine and dipeptides to yield tripeptides; this is the first report of a peptide ligase utilizing dipeptides as nucleophiles.

Conformation analysis of d-glucaric acid in deuterium oxide by NMR based on its JHH and JCH coupling constants.

d-Glucaric acid (GA) is an aldaric acid and consists of an asymmetric acyclic sugar backbone with a carboxyl group positioned at either end of its structure (i.e., the C1 and C6 positions). The purpose of this study was to conduct a conformation analysis of flexible GA as a solution in deuterium oxide by NMR spectroscopy, based on J-resolved conformation analysis using proton-proton ((3) JHH ) and proton-carbon ((2) JCH and (3) JCH ) coupling constants, as well as nuclear overhauser effect spectroscopy (NOESY). The (2) JCH and (3) JCH coupling constants were measured using the J-resolved heteronuclear multiple bond correlation (HMBC) NMR technique. NOESY correlation experiments indicated that H2 and H5 were in close proximity, despite the fact that these protons were separated by too large distance in the fully extended form of the chain structure to provide a NOESY correlation. The validities of the three possible conformers along the three different bonds (i.e., C2C3, C3C4, and C4C5) were evaluated sequentially based on the J-coupling values and the NOESY correlations. The results of these analyses suggested that there were three dominant conformers of GA, including conformer 1, which was H2H3:gauche, H3H4:anti, and H4H5:gauche; conformer 2, which was H2H3:gauche, H3H4:anti, and H4H5:anti; and conformer 3, which was H2H3:gauche, H3H4: gauche, and H4H5:anti. These results also suggested that all three of these conformers exist in equilibrium with each other. Lastly, the results of the current study suggested that the conformational structures of GA in solution were 'bent' rather than being fully extended. Copyright © 2016 John Wiley & Sons, Ltd.

NMR-based analysis of the chemical composition of Japanese persimmon aqueous extracts.

Japanese persimmon (Diospyros kaki L.) is recognized as an outstanding source of biologically active compounds relating to many health benefits. In the present study, NMR spectroscopy provided a comprehensive metabolic overview of Japanese persimmon juice. Detailed signal assignments of Japanese persimmon juice were carried out using various 2D NMR techniques incorporated with broadband water suppression enhanced through T1 effects (BB-WET) or WET sequences, and 26 components, including minor components, were identified. In addition, most components were quantitatively evaluated by the integration of signals using conventional (1) H NMR and BB-WET NMR. This is the first detailed analysis combined with quantitative characterization of chemical components using NMR for Japanese persimmon. Copyright © 2015 John Wiley & Sons, Ltd.

Achievement of 1 H-19 F heteronuclear experiments using the conventional spectrometer with a shared single high band amplifier.

The (1)H-(19) F heteronuclear NMR experiments were achieved using the conventional spectrometer equipped with a single high band amplifier and a (1)H/(19)F/(13) C double-tuned probe. Although double high band amplifiers are generally required to perform such experiments, a simple modification of pathway in the conventional spectrometer was capable of acquiring various (1)H-(19)F heteronuclear spectra. The efficiency of the present technique was demonstrated in an application for (19)F{(1)H} and (1)H{(19)F} saturation transfer difference experiments.